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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF EPI-X4, A HUMAN ALBUMIN-DERIVED PEPTIDE THAT REGULATES INNATE IMMUNITY THROUGH THE CXCR4/CXCL12 CHEMOTACTIC AXIS AND ANTAGONIZES HIV-1 ENTRY
 
Authors :  J. Perez-Castells, A. Canales, J. Jimenez-Barbero, G. Gimenez-Galle
Date :  18 Mar 15  (Deposition) - 29 Apr 15  (Release) - 20 May 15  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Antagonist, Inhibitor Peptide, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Zirafi, K. A. Kim, L. Standker, K. B. Mohr, D. Sauter, A. Heigele, S. F. Kluge, E. Wiercinska, D. Chudziak, R. Richter, B. Moepps, P. Gierschik, V. Vas, H. Geiger, M. Lamla, T. Weil, T. Burster, A. Zgraja, F. Daubeuf, N. Frossard, M. Hachet-Haas, F. Heunisch, C. Reichetzeder, J. L. Galzi, J. Perez-Castells, A. Canales-Mayordomo, J. Jimenez-Barbero, G. Gimenez-Gallego, M. Schneider, J. Shorter, A. Telenti, B. Hocher, W. G. Forssmann, H. Bonig, F. Kirchhoff, J. Munch
Discovery And Characterization Of An Endogenous Cxcr4 Antagonist.
Cell Rep V. 11 737 2015
PubMed-ID: 25921529  |  Reference-DOI: 10.1016/J.CELREP.2015.03.061

(-) Compounds

Molecule 1 - SERUM ALBUMIN
    ChainsA
    FragmentALBUMIN 3 DOMAIN RESIDUES 432-447
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2N0X)

(-) Sites  (0, 0)

(no "Site" information available for 2N0X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2N0X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2N0X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013017R434CALBU_HUMANPolymorphism78575701AR3C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_013017R434CALBU_HUMANPolymorphism78575701AR3C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2N0X)

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002958972aENSE00002075693chr4:74269956-74270123168ALBU_HUMAN1-27270--
1.3aENST000002958973aENSE00001076782chr4:74270833-7427089058ALBU_HUMAN27-46200--
1.4bENST000002958974bENSE00001076799chr4:74272346-74272478133ALBU_HUMAN46-90450--
1.5aENST000002958975aENSE00001076811chr4:74274311-74274522212ALBU_HUMAN91-161710--
1.7dENST000002958977dENSE00001076808chr4:74275072-74275204133ALBU_HUMAN161-205450--
1.8aENST000002958978aENSE00001076797chr4:74276029-7427612698ALBU_HUMAN206-238330--
1.9aENST000002958979aENSE00001076788chr4:74277713-74277842130ALBU_HUMAN238-281440--
1.10bENST0000029589710bENSE00001076792chr4:74279137-74279351215ALBU_HUMAN282-353720--
1.11aENST0000029589711aENSE00001076805chr4:74280752-74280884133ALBU_HUMAN353-397450--
1.12ENST0000029589712ENSE00001076781chr4:74281973-7428207098ALBU_HUMAN398-430330--
1.13bENST0000029589713bENSE00001076796chr4:74283248-74283386139ALBU_HUMAN430-476471A:1-1616
1.14bENST0000029589714bENSE00001076790chr4:74283805-74284028224ALBU_HUMAN477-551750--
1.16bENST0000029589716bENSE00001076802chr4:74285224-74285356133ALBU_HUMAN551-595450--
1.18aENST0000029589718aENSE00001076795chr4:74285971-7428603868ALBU_HUMAN596-609140--
1.20jENST0000029589720jENSE00001823230chr4:74286809-74287129321ALBU_HUMAN-00--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:16
 aligned with ALBU_HUMAN | P02768 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:16
                                   441      
           ALBU_HUMAN   432 LVRYTKKVPQVSTPTL 447
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ................ Sec.struct. author
                 SAPs(SNPs) --C------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
               Transcript 1 Exon 1.13b       Transcript 1
                 2n0x A   1 LVRYTKKVPQVSTPTL  16
                                    10      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2N0X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2N0X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2N0X)

(-) Gene Ontology  (45, 45)

NMR Structure(hide GO term definitions)
Chain A   (ALBU_HUMAN | P02768)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016209    antioxidant activity    Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0005504    fatty acid binding    Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0015643    toxic substance binding    Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0015721    bile acid and bile salt transport    The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0009267    cellular response to starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
    GO:0019836    hemolysis by symbiont of host erythrocytes    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0042157    lipoprotein metabolic process    The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
    GO:0051659    maintenance of mitochondrion location    Any process in which a mitochondrion is maintained in a specific location within a cell and prevented from moving elsewhere.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0043069    negative regulation of programmed cell death    Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0046010    positive regulation of circadian sleep/wake cycle, non-REM sleep    Any process that activates or increases the duration or quality of non-rapid eye movement (NREM) sleep.
    GO:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
    GO:0046689    response to mercury ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mercury ion stimulus.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
    GO:0010033    response to organic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus.
    GO:0070541    response to platinum ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a platinum stimulus.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
    GO:0043252    sodium-independent organic anion transport    The directed, sodium-independent, movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ALBU_HUMAN | P027681ao6 1bj5 1bke 1bm0 1e78 1e7a 1e7b 1e7c 1e7e 1e7f 1e7g 1e7h 1e7i 1gni 1gnj 1h9z 1ha2 1hk1 1hk2 1hk3 1hk4 1hk5 1n5u 1o9x 1tf0 1uor 1ysx 2bx8 2bxa 2bxb 2bxc 2bxd 2bxe 2bxf 2bxg 2bxh 2bxi 2bxk 2bxl 2bxm 2bxn 2bxo 2bxp 2bxq 2esg 2i2z 2i30 2vdb 2vue 2vuf 2xsi 2xvq 2xvu 2xvv 2xvw 2xw0 2xw1 2ydf 3a73 3b9l 3b9m 3cx9 3jqz 3jry 3lu6 3lu7 3lu8 3sqj 3tdl 3uiv 4bke 4e99 4emx 4g03 4g04 4hgk 4hgm 4iw1 4iw2 4k2c 4k71 4l8u 4l9k 4l9q 4la0 4lb2 4lb9 4n0f 4n0u 4s1y 4z69 5fuo 5id7 5ifo 5ijf 5ujb 5x52

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